Showing posts with label etymology. Show all posts
Showing posts with label etymology. Show all posts

May 9, 2008

Big bacteria with lots of DNA

Thiomargarita
Size matters.

That's why there are no insects as big as horses [*], or bacteria as large as to be seen without the use of a microscope. Well, actually, the latter is not true —although a typical bacterial cell is not longer than 5 micrometers, a few species such as Thiomargarita namibiensis (left image) and Epulopiscium fishelsoni may reach a length of over 0.5 millimeters (500 micrometers); enough to become visible to the naked eye.

Big bacteria enjoy some advantages; for instance, they can not be swallowed by most predators (such as ciliates) that feed on smaller cells. But they also face important problems, especially those related to diffusion limitation. In general, bacteria obtain their food molecules by diffusion; for this reason, their cells need to maintain a high surface-to-volume ratio. Thiomargarita solves this problem by creating a huge central vacuole that fills about 98% of the cell volume, leaving only a thin layer of cytoplasm lining the cell wall. However, Epulopiscium appears to have a low surface-to-volume ratio (despite the presence of many invaginations of its cell membrane). This anomaly might be partially explained by the fact that Epulopiscium lives in the gut of a tropical fish, presumably a very rich medium (that is, a high concentration of nutrients may compensate their poor diffusion into a big cell). Additionally, this bacterium has some peculiarities that may be related to this issue: it reproduces by forming internal daughter cells (see figure below), and most of its DNA is arranged around the periphery of the cytoplasm.

Life cycle of Epulopiscium
ResearchBlogging.orgRemarkably, a recent article published on PNAS reports that each Epulopiscium cell has tens of thousands of copies of the genome. Because so far nobody has been able to culture Epulopiscium, the authors had to collect some tropical fishes (Naso tonganus, a unicorn fish) on reefs around Lizard Island, Australia. Then, they extracted the intestinal contents, and handpicked thousands of individual Epulopiscium cells with the aid of a microscope and a micropipettor (an automated device for pipetting microliter volumes). Finally, the researchers used quantitative PCR (Polymerase Chain Reaction) to enumerate the copy number of certain genes on individual cells and in DNA obtained from populations of cells. Epulopiscium large cells contained about 250 picograms (pg) of DNA (compare to 6 pg of DNA in a human diploid cell!), corresponding to several tens of thousands of copies of a ≈3.8 megabase genome.

Such an extraordinarily high number of genome copies per cell could be related to Epulopiscium evolution in a number of interesting ways. Given the biased distribution of DNA within the cytoplasm, these big cells might possess a functional compartmentalization. In the authors' words:

"In this way, a large bacterium could function like a microcolony, with different regions of the cell independently responding to local stimuli, which would alleviate some of the pressure to remain small for the sake of rapid intracellular diffusive transport."
The article ends with:
"The enormous, polyploid Epulopiscium cell has converged on the advantages of social microbes but with additional benefits (exceptional motility, enhanced resistance to predation) normally found in large eukaryotic microbes or multicellular organisms."
Epulopiscium: another fascinating microbe!


Original article:
Mendell, J.E., Clements, K.D., Choat, J.H., Angert, E.R. (2008). Extreme polyploidy in a large bacterium. Proceedings of the National Academy of Sciences USA, 105(18), 6730-6734. DOI: 10.1073/pnas.0707522105


Related links:

[*] Giant insects might reign if only there was more oxygen in the air, EurekAlert.


+++++++++++++++++++++++++++++++++++++++++++++++++++++++
Etymology of species names:

Epulopiscium
= “guest at a fish's banquet”
(Latin epulo [sumptuous food, banquet] + piscium [of a fish])

fishelsoni
= "of Fishelson"
(in honor of Lev Fishelson [Tel Aviv University, Israel], one of the discoverers of Epulopiscium)

Thiomargarita
= "sulfur pearl"
(Greek thio [sulfur] + margarita [pearl])

namibiensis
= "from Namibia"

(Please correct me if I'm wrong)
+++++++++++++++++++++++++++++++++++++++++++++++++++++++


Image sources:
Thiomargarita, at the cover of Science (April 16, 1999). The photomicrograph shows three cells under polarized light (middle cell is ~0.2 mm in diameter), and the small yellow spheres are sulfur globules that are restricted to the thin outer layer of the cell. Image: Ferran Garcia-Pichel.
● Life cycle of Epulopiscium. Reprinted by permission from Macmillan Publishers Ltd: Nature Rev. Microbiol. 3, 214-224 (2005). Copyright 2005.

Read the rest of the article >>>

Feb 1, 2008

Anthropomicrobiology

Microbiology TodayThe current issue (February 2008) of Microbiology Today includes a number of articles devoted to the microorganisms that live in our body. In an introductory article (Life on us), Robin Weiss writes:

"As an ecosystem, it has become clear that we are only part human, because a significant amount of our biomass is microbial. In demographic terms, microbes outnumber our own cells. While there are 1014 human cells in the average adult, there are probably ~1015 bacteria and >1017 viruses associated with the human body. In terms of genetic diversity and complexity, the microbial metagenome of humans may be greater than the 3×109 base pairs of human DNA."

So, we are superorganisms, composed of many organisms. In fact, it seems that the collective genome of our microbial symbionts (the microbiome) may contain over 100 times as many genes as our own genome, and provides traits that humans did not need to evolve on their own (from an article in Science).

In Life on us, the author makes another thought-provoking remark:
"Thus while we share >98 % host DNA sequence similarity with the chimpanzee, the microbial and viral species that live on or on us are only ~50 % shared with the great apes."
Definitely, those tiny passengers in our bodies should have influenced our evolution. How much of our "humanity" (whatever makes us different from other apes) do we owe to our microbial cells??

*********************************************

A collection of related links (in chronological order, newest first):
*********************************************

Etymological addendum:

Anthropomicrobiology = anthropo + microbiology
Microbiology = micro + biology
Biology = bio + logy
*********************************************

Read the rest of the article >>>

Jan 23, 2008

Phytochemistry Letters

Phytochemistry LettersThe Phytochemical Society of Europe and Elsevier have given birth to a new journal, Phytochemistry Letters, which will cover all aspects related to natural products. Submissions from any field of natural product research are encouraged, including: structural elucidation of natural products, clinical efficacy, safety and pharmacovigilance of herbal medicines, natural product biosynthesis and chemical synthesis, chemical ecology, biotechnology, pharmacology, metabolomics, ethnobotany and traditional usage, natural product metabolism, genetics of natural products...
Despite the "phyto-" (= plant) in its name, the journal will not deal only with natural products from plants, but also with those from microorganisms (one of the editors is specifically associated to the subject of "microbial natural products").

Read the rest of the article >>>

May 5, 2007

Actinomycetes, natural drug factories

Actinomycetes are Gram-positive bacteria with a high GC-content in their DNA. Among others, representative genera include Corynebacterium, Micrococcus, Mycobacterium, Nocardia, Propionibacterium, and Streptomyces. Many actinomycetes, such as Streptomyces, grow as branching filaments and live in soil, as fungi do. Because of this resemblance, actinomycetes were originally classified as fungi. This was reflected on their name, where "mycetes" comes from the Greek for "mushroom, fungus".

Some actinomycetes are pathogenic, such as
Mycobacterium tuberculosis. However, many others are extremely useful due to their ability to produce compounds with pharmaceutical properties (antibiotic, antifungal, antitumor, immunosuppressive). The genus Streptomyces is well known precisely for this ability.

In this blog, I intend to post mainly about the biology of actinomycetes, especially those aspects related to the biosynthesis of natural products of pharmaceutical interest. However, I may occasionally deviate from the primary theme. There might be some microbiology, some biochemistry, some chemical biology, some genetics...

Oh, about the title: "Twisted Bacteria". No, it's not that they are "perverted" (although some times we researchers in the field may think so...). The title was inspired by the word "
Streptomyces", where "strepto" comes from the Greek for "twisted, twined".

(Image: Streptomyces sp. under the microscope. CDC/Dr. David Berd, Public Health Image Library)

Read the rest of the article >>>

Creative Commons License Except where otherwise noted, blog posts by Cesar Sanchez in Twisted Bacteria are licensed under a Creative Commons Attribution 3.0 Unported License. Please let me know if any quotes or images on this blog are improperly credited. E-mail: TwistedBacteria AT gmail DOT com . Social media icons by Oliver Twardowski and AddThis.